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Carolyn Larabell, Director of the National Center for X-Ray Tomography (NCXT) has been selected by the ALS Users’ Executive Committee to receive the 2017 David A. Shirley Award for Outstanding Scientific Achievement at the ALS.

Plant biologists have sequenced the genome of a particularly promising species of green alga, providing a blueprint for new discoveries in producing sustainable biofuels, antioxidants, and other valuable bioproducts.

The researchers targeted Chromochloris zofingiensis, a single-celled green alga that has drawn commercial interest as one of the highest producers of the best lipids for biofuel production.

The team of scientists, led by researchers at the Department of Energy’s (DOE) Lawrence Berkeley National Laboratory (Berkeley Lab) in collaboration with the University of California, Los Angeles, recently published their work in the Proceedings of the National Academy of Sciences. It is also available on Phytozome, the DOE Joint Genome Institute’s Plant Genomics Portal.

The project was conceived of and developed at Berkeley Lab by Krishna Niyogi, faculty scientist and an investigator at the Howard Hughes Medical Institute.
“This genome will be an important resource to develop renewable and sustainable microalgal biofuels to facilitate clean energy and a cleaner environment,” said study lead author Melissa Roth, a postdoctoral researcher in Niyogi’s lab. “Algae absorb carbon dioxide and are intrinsically solar-powered by photosynthesis, but C. zofingiensis has an added benefit in that it can be cultivated on non-arable land and in wastewater.”

Niyogi also pointed out that C. zofingiensis is a natural source for astaxanthin, an antioxidant derived from dietary algae that gives salmon its pinkish hue. In algae, astaxanthin is thought to provide protection from oxidative stress.

“This alga has potential as a nutraceutical,” said Niyogi, who is also a UC Berkeley professor of plant and microbial biology. “Studies are already underway to determine whether astaxanthin’s anti-inflammatory properties are beneficial in treatments for cancer, cardiovascular disease, neurodegenerative disease, diabetes, and other human health problems.”

To get an inside look at the cells, the researchers relied upon the National Center for X-ray Tomography (NCXT), a joint Berkeley Lab-UCSF program located at the Lab’s Advanced Light Source. Using soft X-ray tomography, a technique comparable to a computerized tomography scan, scientists imaged and then reconstructed sections of the algal genome to generate a 3-D view. Cells were captured dividing into two, four, and even sixteen daughter cells.

“Combining multiple sequencing techniques, we were able to generate a chromosome-level assembly of the genome, which is an uncommonly high level of architecture for an alga and similar to that of a model organism. In fact, the quality of the C. zofingiensis genome rivals the model green alga Chlamydomonas reinhardtii, which was first sequenced about a decade ago,” said Roth. The alga contains approximately 15,000 genes. Other senior authors on the paper include Sabeeha Merchant, UCLA professor of biochemistry; Matteo Pellegrini, UCLA professor of molecular, cell, and developmental biology; and Carolyn Larabell, NCXT director and professor of anatomy at UCSF.

This research was supported by DOE’s Office of Science, the US Department of Agriculture, the National Institute of General Medical Sciences, and the Gordon and Betty Moore Foundation. The Advanced Light Source is a DOE Office of Science User Facility. NCXT is jointly funded by DOE and the National Institutes of Health.

NCXT staff and collaborators have mapped the reorganization of genetic material that takes place when a stem cell matures into a nerve cell. Detailed 3-D visualizations show an unexpected connectivity in the genetic material in a cell’s nucleus, and provide a new understanding of a cell’s evolving architecture.
These unique 3-D reconstructions of mouse olfactory cells, which govern the sense of smell, were obtained using soft x-ray tomography. The results could help us understand how patterning and reorganization of DNA-containing material called chromatin in a cell’s nucleus relate to a cell’s specialized function as specific genes are activated or silenced.

During mitochondrial fission, the mitochondrial outer membrane proteins Mff, MiD49 and MiD51 recruit Drp1 to execute organelle constriction. Intriguingly, recent studies indicate that endoplasmic reticulum (ER) tubules can wrap around mitochondria and mediate membrane constriction in a Drp1-independent manner, but it is still unclear whether other proteins are involved. To investigate whether MiD49 and MiD51 are linked to the role of the ER in mitochondrial fission, Kirstin Elgass and colleagues (p. 2795) used live-cell confocal imaging, correlative cryogenic fluorescence microscopy (CRM) and soft X-ray tomography (SXT) to render a 3D reconstruction of ER–mitochondria contact sites. They observed that MiD49 colocalised with Mff, and MiD51 colocalised with Mff and Drp1. Both MiD proteins formed dynamic foci that were found both within and outside of constriction sites, and within sites that underwent repeated constriction–expansion cycles. The authors then established that mitochondria–ER contact sites colocalise with MiD foci, but that only 40% of these contacts were at constriction sites. Using CRM-SXT they next reconstructed the 3D ER–mitochondria landscape, and found that the ER forms short extensions that contact the mitochondria at MiD foci, the length of which was under the limit of resolution for confocal microscopy. Therefore, besides showing that ER tubules contact mitochondria at MiD foci, this study also employs a novel imaging approach that could be extremely useful for high-resolution studies of intracellular structures.

As part of the CSH Single Cell Analysis Course, the NCXT offered a multi-day workshop on soft x-ray tomography (SXT). Attendees had the opportunity to gain hands-on experience of working with SXT data, including sophisticated techniques, such as segmenting reconstructed cells. More details and photos of the team in action are here.

Josie - a graduate student in the Lomvardas lab - was awarded the Kaluza Prize at the 2014 ASCB. The prize is in recognition of her breakthrough work on olfactory neurons, which included soft x-ray tomography of neurons carried out at the NCXT. Read more about Josie here

Associate Professor of Mathematics and Statistics Sam Isaacson has been awarded a CAREER Award in Mathematics by the National Science Foundation. It is a prestigious five-year grant, given annually to the top 20-30 tenure-track mathematicians nationally.

This award will fund the development of new numerical methods for simulating how proteins and mRNAs move about and interact within cells. These new methods are designed to allow the study of cellular processes, such as gene expression and signal transduction, in realistic three-dimensional models of the cellular space. An important feature of these models is the incorporation of explicit representations of cellular organelles and membrane surfaces, reconstructed from high resolution soft x-ray tomography data (courtesy C. Larabell at UCSF). The algorithms and computer programs made available by this research will enable more in depth studies of many pathways involved in cell signaling, growth, division, tissue development, and cancer proliferation.

The grant will also support the development of a more comprehensive mathematical biology program within the Department of Mathematics and Statistics. A new “Mathematical Biology on Clusters” course will be created to teach the process of computational model development for biological problems requiring the use of large datasets and large-scale computing resources. The new simulation tools we develop will be integrated into this course, enabling course projects in which students study models of specific cellular processes within their own cell (reconstructed from soft x-ray tomography data).

The award shows that there is substantial interest in developing new methods with which to model the spatial movement and interaction of proteins within cells. I’ve been interested in these questions for many years, but it is only recently that the needed computational resources, experimental data, and appropriate numerical methods to facilitate such modeling are becoming available. The planned research is one mathematical step in the long journey toward creating accurate, dynamic, three-dimensional in silico models of single cells from high-throughput and high resolution imaging data.